RnoINT0143836 @ rn6
Intron Retention
Gene
ENSRNOG00000016687 | Ssc5d
Description
scavenger receptor cysteine rich family member with 5 domains [Source:RGD Symbol;Acc:1565772]
Coordinates
chr1:72457908-72459023:-
Coord C1 exon
chr1:72458715-72459023
Coord A exon
chr1:72458226-72458714
Coord C2 exon
chr1:72457908-72458225
Length
489 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
CCTCTGTCCTTCCGTTTCAGGTC
3' ss Score
13.67
Exon sequences
Seq C1 exon
AGCGGCTGCGTCTGGTCTCAGGTCCCCATGGATGTGCCGGCCGCCTGGAAGTCTGGCACGGTGGACGTTGGGGTACTGTCTGCGATGATGGATGGGACCTCCGAGACGCAGCAGTGGCCTGTAGGGAGCTAGGATGTGGGGGAGCGCTGGCCGCCCCTGGAGGTGCCAGATTCGGACCTGGTGAGGGACCCGTGTGGATGGACGATGTCGGGTGTGGAGGAGGAGAGGAGGCCCTCCGGGACTGTCCCCGAAGCCCCTGGGGCCGGAGCAACTGTGACCACACAGAGGATGCAGGGCTGGTCTGTACTG
Seq A exon
GTATGTGTGTGGGGGGGTGGGGGGGGCAACTACTTCCTCTTCAGATCTCAGCTCCCCCCTGCCCCCAGGAAGCAGTAAAAGGCCTGGCCTCACGTCTGTCTCTCTATACATTCTCTGGGAGAGGCAGTGAGGATCTTAGCATGTCGAGTCTCAGTTTTCTTGAGGAAGCAACTAGAAACTGGGACCAAGTGTTAAGGGCCATGGAAGGGCACTTGGGGGCTTCCTCCTCCATTCTCTCCTTCTTCTTCTACCTCACTTCCTTTCCCTCTTTCCTTCCCCCAGCGTTCTTGTTCCCTGTCGGCGTAAGTCAATACCTGTTCACCCATCCTGCTTCTTCACTGGTCTAACTCAGTATCTGCTCACAACCCTAGACTCCCACGGTGTTAAGGTGACCCTTGCAAACCCACTGTAGTTTTCCTTCTTGGTTACATAGCAGGCACTCGTCCATTCTGACCTCTTGTCACCCTGACCTCTGTCCTTCCGTTTCAG
Seq C2 exon
GTCCTGCACCCAGGTTGCGCCTTGCTGATGGTCCCCACGGCTGTGCTGGGCGCCTGGAGGTTTGGCATGGTGGCCGCTGGGGGTCGGTATGTGACGATGCTTGGGATCTTCGTGATGCCGCTGTGGCCTGCAGGGAGCTGGGCTGTGGGGGTGCCCTGGCTGCCCCAGGGGGTGCCTTCTTTGGTGAGGGGGCTGGACCCATCATCCTGGATGACCTCAGATGTCGAGGAAACGAGACAGCCTTACGATTCTGCCCTGCGAGGCCCTGGGGTCAGCATGACTGTCACCATCGGGAGGATGCTGGGGCTGTGTGTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016687:ENSRNOT00000022480:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.139 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=94.2)
A:
NA
C2:
PF0053013=SRCR=WD(100=91.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGATGGATGGGACCTCCGA
R:
GCATCACGAAGATCCCAAGCA
Band lengths:
344-833
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]